Abstract

A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. While several tools exist to intersect and visualize sets of genes, similar tools dedicated to the visualization of genomic regions sets are currently limited. To fill this gap, we have developed Intervene, which provides an easy and automated interface for effective intersection and visualization of genomic region sets, thus facilitating their analysis and interpretation. Intervene contains three modules: venn to generate Venn diagrams of up-to 6 sets, upset to generate UpSet plots of more than 3 sets, and pairwise to compute and visualize intersections of genomic sets as clustered heatmap. Intervene is implemented in Python and R and is freely available at https://bitbucket.org/CBGR/intervene with a Shiny App at https://asntech.shinyapps.io/intervene